User: chjiao3456

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chjiao345640
Reputation:
40
Status:
New User
Location:
Michigan State University, USA
Last seen:
3 years, 4 months ago
Joined:
8 years, 4 months ago
Email:
c*********@gmail.com

 PhD student in MSU, majored in Computer Science & Engineering, research area is bioinformatics.

Posts by chjiao3456

<prev • 39 results • page 1 of 4 • next >
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Comment: C: How to tell the mismatches come from sequencing errors or a different haplotype?
... Yes, similar like that. Two strains of HIV-1 virus are combined for sequencing. ...
written 3.4 years ago by chjiao345640
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Comment: C: How to tell the mismatches come from sequencing errors or a different haplotype?
... Thanks for your suggestions. The 95% and 5% mean the percentage of reads number corresponding to the dominant and minor haplotypes, respectively. Unfortunately, there are no barcodes for the two haplotypes. ...
written 3.4 years ago by chjiao345640
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How to tell the mismatches come from sequencing errors or a different haplotype?
... Hi everyone, I have a next-generation sequencing data set of two haplotypes. One is of 95% and the other one is only 5% of the sequencing data. I used assembly methods to get the dominant haploytpe, and then I mapped the raw reads to the assembled contigs. Since the sequence similarity between two h ...
mismatches haplotype sequencing written 3.4 years ago by chjiao345640
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Comment: C: Jellyfish Installation Question
... I am trying to install Jellyfish, however I was stuck in the first step for there is no configure file at all... ...
written 3.9 years ago by chjiao345640
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Answer: A: Tools to remove duplicate or substring reads
... Just noticed that SGA tool is able to do this. https://www.biostars.org/p/80970/ ...
written 3.9 years ago by chjiao345640
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Comment: C: Tools to remove duplicate or substring reads
... Thanks for your help. I have added examples in the question. ...
written 3.9 years ago by chjiao345640
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Tools to remove duplicate or substring reads
... Is there any efficient tool to remove substring reads or duplicate reads from NGS data set? I know that readjoiner could remove the duplicated reads, but seems not work on substring reads. Thanks. Example: Duplicates: read1: AGTCAT read2: AGTCAT In this case, only one read will be kept. Substrin ...
next-gen alignment sequencing written 3.9 years ago by chjiao345640
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Readjoiner prefilter removed reads
... Hi, I am using the Readjoiner to produce the overlap graph for my sequencing data. Is there any way to get the removed duplicate reads in the first prefilter step? I am applying the pair-end information for my analysis, so I would like to keep the information of every reads. Thanks. ...
next-gen sequencing written 4.5 years ago by chjiao345640
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Comment: C: Chip-Seq, Get Highly Enriched Regions For A Certain Mark Within One Sample
... Shall we consider the length of the region? I guess the P-value should be calculated as: Pval = Possion (X>=k; lambda*region_length) ...
written 4.7 years ago by chjiao345640
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Comment: C: State of art gene prediction tools for grass genomes
... Thank you. So do you mean usually there are no specific tools for grass genes prediction? ...
written 5.4 years ago by chjiao345640

Latest awards to chjiao3456

Popular Question 4.4 years ago, created a question with more than 1,000 views. For The Hardware Request For Repeatmasker
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Adapter for RNA-seq alignment
Popular Question 4.9 years ago, created a question with more than 1,000 views. For The Hardware Request For Repeatmasker
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Should Rna-Seq Reads Map To One Strand Of Cdna Reference?
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